public class CellomicsReader extends FormatReader
| Modifier and Type | Field and Description |
|---|---|
static int |
C01_MAGIC_BYTES |
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSIONCOMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixesCAN_GROUP, CANNOT_GROUP, MUST_GROUP| Constructor and Description |
|---|
CellomicsReader()
Constructs a new Cellomics reader.
|
| Modifier and Type | Method and Description |
|---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
int |
fileGroupOption(String id)
Returns an int indicating that we cannot, must, or might group the files
in a given dataset.
|
String[] |
getDomains()
Returns the list of domains represented by the current file.
|
String[] |
getSeriesUsedFiles(boolean noPixels)
Returns an array of filenames needed to open the current series.
|
protected void |
initFile(String id)
Initializes the given file (parsing header information, etc.).
|
boolean |
isThisType(RandomAccessInputStream stream)
Checks if the given stream is a valid stream for this file format.
|
byte[] |
openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
Obtains a sub-image of the specified image plane
into a pre-allocated byte array.
|
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadata, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeriescheckSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixesclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetFormat, getNativeDataType, getSuffixespublic static final int C01_MAGIC_BYTES
public boolean isThisType(RandomAccessInputStream stream) throws IOException
IFormatReaderisThisType in interface IFormatReaderisThisType in class FormatReaderIOExceptionpublic String[] getDomains()
IFormatReadergetDomains in interface IFormatReadergetDomains in class FormatReaderpublic byte[] openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
throws FormatException,
IOException
IFormatReaderopenBytes in interface IFormatReaderopenBytes in class FormatReaderno - the image index within the file.buf - a pre-allocated buffer.x - X coordinate of the upper-left corner of the sub-imagey - Y coordinate of the upper-left corner of the sub-imagew - width of the sub-imageh - height of the sub-imagebuf for convenience.FormatException - if there was a problem parsing the metadata of the
file.IOException - if there was a problem reading the file.IFormatReader.openBytes(int, byte[], int, int, int, int)public void close(boolean fileOnly)
throws IOException
IFormatReaderCloseable.close().close in interface IFormatReaderclose in class FormatReaderIOExceptionpublic String[] getSeriesUsedFiles(boolean noPixels)
IFormatReadergetSeriesUsedFiles in interface IFormatReadergetSeriesUsedFiles in class FormatReaderpublic int fileGroupOption(String id) throws FormatException, IOException
IFormatReaderfileGroupOption in interface IFormatReaderfileGroupOption in class FormatReaderFormatExceptionIOExceptionprotected void initFile(String id) throws FormatException, IOException
FormatReaderinitFile in class FormatReaderFormatException - if a parsing error occurs processing the file.IOException - if an I/O error occurs processing the fileCopyright © 2014 Open Microscopy Environment